Clara Gone Missing
by arminius15
Summary: I suck at Summaries but here I go: Clara wants to take a break but the Doctor has enemies who wants revenge on him. And their way of doing that is attacking and kidnapping Clara. What will the Doctor do to save Clara.
1. Clara

**Chapter 1: Clara**

Clara and the Doctor walked back into the Tardis after ending another problem in the universe. "Where do you want to go now Clara?" Clara was thinking of where she wanted to go. Of Course Clara knew where she wanted to go, she wanted a break and go back to work. "Doctor, can I ask you something?" Clara asked nervously. "If it's a hug you're not getting one." He waited for a slight chuckle and looked up at her to find her expression a serious one.

"Doctor, can I have a break from traveling?" Clara asked nervously but with a serious face, she knew that the Doctor and she have created more dangerous enemies including older ones. "Clara, I don't think it's wise for you to off on your own." Clara sighed, "Please Doctor? Just for five days?" the Doctor had a worried expression, she knew he didn't want to lose, and for her to be hurt. "Fine," he said with a sigh. Clara dropped the serious face and smiled with her eyes sparkling in excitement. The Doctor punched in the coordinates to bring Clara home. When they landed the Doctor pulled out a necklace that Clara saw right away. "What's that for?" Clara asked. "It's a tracker necklace for you." The Doctor said.

"It lets me know where you are on what planet. "Alright Doctor, I'll never take it off." Clara walks over and grabs the necklace and puts it on. "Bye Doctor," she says before opening the Tardis. "Clara, be careful." She was still smiling when she said "I'll be careful." The Doctor was still very worried about her, "I mean it Clara." She replied with "I'll call you if anything goes wrong." Then she exited out of the Tardis. Leaving the Doctor worried that would probably haunt him if Clara got hurt. Clara was ready for her break from traveling; she was dropped off in the parking lot by her flat. When she got in her flat she found it destroyed, she was angry until she heard a big crash, she was scared. She wasn't alone, she felt her tracker necklace throbbing, it probably meant it picked up an enemy target.

Of all the creatures it was Zygons, it was coming after her. Clara grabbed the nearest sharp object to protect herself. Of course she should run out and call the Doctor but too late, the Zygon ran toward Clara, grabbed her and threw Clara against the wall. Clara felt the pain as soon as she made contact with the wall. She felt dizzy but got up ready to run away from the Zygon. Clara grabbed a hand held mirror and threw it at the Zygon. It stalled the Zygon so Clara could run outside and call the Doctor.

Clara was in pain, surely bruised then she felt her arm was wet. She removed her hand and it was painted red with blood. She quickly pulled out her phone to call the Doctor. She waited for him to pick up, her head was throbbing and her cut was dripping blood. Then he answered but Clara was slowing fading unconscious. "Clara?" he asked. "Clara your necklace tells me you are outside of your flat." Clara was gasping for air "Doctor…help," she took a big gasp of air. "I'm…injured and attacked." Then Clara fell unconscious.

"Clara!" he yelled frantically through the phone. Then he heard a voice, as it got closer to the phone it said "The Zygons have Clara, Doctor come find her before she dies." The Doctor immediately punched in the coordinates to where Clara's necklace says. "I'm coming Clara, don't worry."

 **I know most of you out there have noticed that I have deleted stories but, starting from now on I will be posting stories that I write down in notebooks. My first one is obviously Doctor Who. I will be writing more Doctor who stories, Sherlock, Mortal Instruments, And Infernal Devices. But yea I am just having a terrible teenage life right now. I have so much stress that it goes to my lower back. Anyways I have marching band and my mom is trying to find a job and we are real tight on money. And that is hard for my family. But anyways I will still gladly be posting stories. Also I will try to post stories once a week or sometimes every other week. (P.S. disclaimer I do not own Doctor Who and I am going to make these chapters not long but not too short)**


	2. Missing In Action

**Hi guys, I'm so sorry for not posting anything in awhile. Not to be a complainer or anything its just marching band has made my month busy, but today I will add a chapter. Please enjoy**

 **Chapter 2: Missing In Action**

As soon as the TARDIS settled on the ground he ran out the door to see if Clara was nearby. As he took his first step out of the TARDIS he stepped in a puddle of blood, of course he assumed it was Clara's for she was nowhere to be seen. He stopped and stared in horror at the amount of blood on the pavement. That made him snap to run to her flat to see what he could find. Right at the front of her flat, her door was ripped to shards of wood. He walked in carefully to make sure he didn't trip over the mess and then he saw the wall that had a shelf on it but the shelf was now collapsed to pieces on the floor with blood on it. It looked the same color of blood out on the pavement.

"Clara was right, she was injured…and badly." Then the Doctor's phone began to ring. He quickly pulled it out and answered it. "What do you want Kate? I'm a little busy." Kate sighed in annoyance. "Don't hide it from me Doctor. We know Clara has been taken and also billion of people with the same kind of attack Clara had." "How do you know Clara was attacked?" Kate didn't say anything for a few seconds. "That's because I have a squad is here to collect clues from Clara's flat. The Doctor just stood there and didn't say a thing. "Don't worry Doctor, we will solve this together on why the Zygons are attacking again."

The Doctor sighed, "That's what I'm afraid of." He hung up the phone and walked back to the TARDIS.

-MEANWHILE-

Clara woke up in a warehouse with her hands tied with chains above her head. The chain was connected to the ceiling of the warehouse. Her vision was blurry and she was confused, then it hit her. She was attacked by Zygons once again. And the next hit was wondering how worried to Doctor was searching for her. She tried to move but her side was causing extreme pain and she realized she wasn't the only one in the warehouse, there were others hanging by chains around her.

Clara didn't know what to do, she was in pain, and terrified. She had to find a way out of the chains but that wasn't going to be easy. So she tried to climb up the chain to somehow unhook the chain, it also was a high climb but Clara had to find a way out of this. She climbed despite of her side telling her not to move because it most likely must be infected.

When she almost got to the top her hands slipped and she fell through the air. The wind got knocked out of her so much she didn't even scream until she almost hit the ground. She woke most other people who were held captive, Clara started to cry because she knew she was alone with know she knew and the Doctor wasn't there to help her. And an infected injury that was causing her so much pain she started to get a fever.

"Where are you Zygons!? Are you just going to hold us captive and watch the rest of the world wonder where in bloody hell we are!"

The Doctor set coordinates for the Tower of London to help solve this case with Kate. When the Doctor arrived Kate was waiting outside the TARDIS. "Doctor, we just a live video call from a secret location. One of my best men is trying to hate the location." Kate led the Doctor to where the live video is being played.

"Doctor, we want war." Said the Zygon on screen just as he saw the Doctor appear. The Doctor wasn't paying much attention to the Zygon he was paying more attention to the hanging people in the background. Then he saw Clara…his two hearts stopped in horror but then he saw that she was alive and awake. "Doctor! Zygons want this peace treaty to end! The Human are killing our own. And if you don't agree to our terms we will kill all these people you see behind us!" the Zygon screamed in anger. The Doctor's face turned pale when he heard if he doesn't and the humans don't listen to their terms his Clara will die right before him.

"What do you exactly want us to do?" asked Kate who took a small glance at the Doctor who clearly was in shock. "We want you to stop searching into our business. That's how your kind started to kill our own and if you don't stop we will kill these humans starting with her. The Doctor and Kate saw that he was pointing at Clara.

Clara quickly looked up and saw the Doctor and Kate on screen and the Zygon pointing at her. Clara took a deep breath and started to slowly and quietly climb up the chain again. That Zygon was so stupid he didn't even notice her climbing. The Doctor tried not to look at her to make sure she didn't fall and get herself caught. "And if you continue we will destroy London." The Doctor looked away from Clara and at the Zygon. "Your kind is already destroying London by taking these people from their friends and family. You took someone very important to me and you will not go down so slow."

The Zygon hissed and laughed. "We are already destroying to London and soon the Humans are next." When he finished his retort to the Doctor, Clara managed to climb to the very top and untie her wrists and slowly slide down the chain but then halfway down the chain unhooked from the roof and Clara fell to the ground unsure of what was going to happen next.

 **I felt like this Chapter could have been better. And for those who enjoyed it I will make more chapters soon.**

 **Disclaimer: I do not own Doctor Who**


	3. On The Run

**Chapter 3: On The Run**

 **Hey guys sorry for making lots of cliffhangers but my cousins from Europe were spending 3 weeks with me. But anyways I will be continuing now also don't forget to leave reviews I like the 4 reviews I have now just don't forget to review.**

The Zygon ended the chat when he heard a thud behind him. Clara had landed on her injured side and got the wind knocked out of her, she gasped for air and she saw the Zygon walking towards her. Clara scrambled up as quickly as she could and ran toward the other side of the warehouse to find an exit. Clara was still gasping for air but near the exit she found a pile of belongings that belonged to the other people hanging around the warehouse including her cell phone with no damage to it. She quickly grabbed her phone and ran out of the warehouse into the pouring rain of London.

She was running around the warehouse area trying to hide somewhere to hide and call the Doctor or Kate. She managed to hide somewhere somewhat dry but was still getting poured on. She grabbed her phone and immediately called the Doctor's phone. The Doctor answered right away, "Clara?" Clara was so relieved to hear his voice she started to cry. "Doctor? I think my side is infected an-and my ribs are broken…" Clara was sobbing; the Doctor didn't care about anything at the moment except for that Clara was alive. "It's alright Clara, Kate tracked your phone and we are on our way to you." Clara was still sobbing, she took a deep ragged breath and said "Doctor…I'm scared."

Then Clara heard the Zygons coming towards her, "Doctor, I got to go… the Zygons are coming." She took a deep breath to relax. "Clara we are almost there hang on." Clara hung up the phone and ran to a different location of the warehouses. Her vision was getting blurry and her heart was racing. She was definitely terrified that what would happen if the Doctor didn't save her in time. But she knew she had to be brave.

Clara found a good hiding spot and thought waiting here for the Doctor would be a good idea. She soon heard a helicopter fly over head then she heard the sound of footsteps. Her body tensed waiting to break for it just in case it wasn't the Doctor. "Doctor I'm scared" she whispered to herself. Her side was crusted with blood from her wound that needed to be cleaned and taken care of. The footsteps stopped and her heart was racing like never before, she knew it must be the Zygons coming to take her back to the warehouse. Then she heard the sound she would never forget, the sound of the Tardis.

Clara was saved by her Doctor. She quietly crawled out of her hiding spot to find the Doctor searching around trying to look for Clara. She tried to stand up but tripped to the ground. The Doctor instantly turned around and saw Clara. Clara looked into his eyes and saw horror, she knew he was looking at her side which was still crusted with blood also her pale face from surviving the drop and her wound. "Clara?! Are you alright?" He ran to her and helped her up to her feet.

"I'm alright Doctor, it's just I think my side is infected." She replied. "It most likely is but don't worry Kate will have you fixed up." Clara could tell there was a little hesitation in his voice but she was just relieved that she was saved. Clara got to the Tardis; the Doctor had put in what looked like a comfortable chair for her to sit when he got her.

He helped Clara sit down then he ran to the controls and punched in the coordinates to the tower of London. When they arrived Clara was walked to a hospital bed and was rolled into a room. The Doctor followed to the room until someone grabbed his arm. "Doctor you can't go in there." Said the person behind him, he turned around and found Kate.

"And why not? It was my fault that she was taken by my enemies." The Doctor replied but almost shouted. "Doctor you must understand that her side is deeply infected, you saw the blood on her side. She is being prepped so they can heal her side." The Doctor said nothing; all he could do was wait for them to heal her side. Kate guided him to a seat outside the door to the room they brought Clara into. The Doctor was tensed, Kate could see that. He was afraid for his friend, she felt bad for him. A few minutes later one of the nurses came out of the room and the Doctor stood up instantly. "She is going to be okay, but she has lost a lot of blood and her side was deeply infected. I'm even surprised she survived, anyways she is asleep now."

"Can we go in Nurse Green?" Kate asked. Nurse Green nodded and they walked in. When they walked in the Doctor was just checking the bag of blood to see if it was going through right then left the room. Clara was in a white hospital gown, her face pale which made her look as if she was sick. The Doctor sat in the chair next to her bed. "Doctor thanks to you and Clara we found the missing people." The Doctor didn't pay attention he just stared at Clara's face waiting for her to wake up.

 **Well another cliffhanger, I'm evil I know but I will continue with a few more chapters. I just don't know how most of these people pull off like 20 chapters for just one big plot; you see I can't do that because I don't have that much of a creative mind so pardon for the short stories I post. Anyways please leave a review I also read them and don't feel shy if you have ideas for the stories I post and the soon stories I like ideas from other people.**

 **Disclaimer: I do not own Doctor Who**


	4. Wake Up

**Chapter 4: Wake Up**

 **Disclaimer: I do not own Doctor Who**

 **Sorry for not updating this story in a long time. But I will try and continue to update this story.**

Clara woke up slowly, she saw the Doctor he was looking out the window. She felt groggy from what happened to her at the warehouse. "Doctor?" Clara asked. Her voice sounded dry then her throat felt really dry.

The Doctor turned around and saw his friend awake but he could tell she was dehydrated. He quickly walked across the room and grabbed a glass and filled it with water from the sink. He set the glass down so he could help her sit up. The Doctor then grabbed the glass and helped her drink the water.

"You were out for about three days." The Doctor said with a little concern.

"I remember, how is my side?" she asked she could feel a little pain but she knew it was certainly infected.

When she mentioned her side the Doctor remembered seeing how bloody it was and crusted. It made him feel uneasy that the Zygons hurt his friend. But they actually got scared off, but he knew that Clara was going to be in bed rest for awhile.

"Doctor, did you save the other people who were in the warehouse?" Clara asked

Kate walked into the room and answered. "Yes"

Clara looked at her and she saw that her whole side was bandaged really well but she could see the red outline of her cut.

"Kate? What am I going to do about my home?" Kate and the Doctor exchanged looks.

"Kate has found a nice flat for you close to the tower of London." The Doctor answered.

"But that isn't exactly close to my work," Clara responded. "But I guess it can work for now." Kate smiled at little.

"I have to leave for a meeting, and Clara you are to stay here for about a few more days, you need recovery from your injury." Kate said then left the room.

Doctor looked out the window again and Clara knew what exactly what he was thinking about. "Doctor I'm sorry about not listening to you about just staying with you in the TARDIS where it was safe but I can't just be kept in a box for the rest of my life."

The Doctor turned around and faced her. "My Clara it's alright, I know I can't keep you in the TARDIS forever but next time I'm stay near you so this doesn't happen again." He pointed at the side that was wrapped up in a bandage.

"So, I'm guessing you already had a look at my flat?" Clara asked the Doctor.

He nodded and turned to look out the window again. "Doctor you can go on adventure, I'll stay put right here." The Doctor smiled but he continued to look out the window.

-A Few Days Later-

A few days passed being cooped up in that room made Clara really want to see her new home. Once she was alright to leave the Doctor brought her to her new Flat. "Doctor this flat looks amazing, but how am I going to pay for this. This flat seems quite expensive?"

The Doctor was looking around as well even though he probably made sure everything in this entire flat was safe. "Kate said something about her paying for it so that I wouldn't lecture her again about keeping my friends and ally's safe."

Clara was smiling and excited to see her bedroom, when she walked in it was huge and wasn't small like her old flat but it was really modern for her taste but she could live with it. "Thanks Doctor, I assume you had a plan on me living closer to the London Tower to keep check on me whenever London is a target again?" Clara asked with humor in her voice.

"Actually yes," The Doctor said. "I know you have just been checked out of the small hospital but do you think you are up for an adventure?"

Clara turned around to face the Doctor and smiled and he knew that smile which meant yes. And then he smiled in reply and they ran for the TARDIS to see what awaits them next.

 **The End, I know it was short but I had a long wait and I felt like the story was over, I will try and make more Doctor Who Stories as I continue but I really enjoyed making this story it was fun and please review.**


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